ABSTRACT
A great promise of atomically detailed simulations is the generality of the model. Molecular dynamics (MD) simulations are used to study highly complex and diverse processes (such as energy ow and conformational transitions in proteins) with essentially the same mathematical model. We call this approach “the standard model of computational biophysics,” or in short “the standard model.” The classical equations of motion are solved with an empirical force eld U(X
Æ ), which is transferable
between different molecular systems. The vector X Æ
points to the positions of all the atoms in the molecular system. The number of atoms that are included in simulations (and the length of the vector X
Æ ) varies from a few hundreds to a submillion, making
these simulations computationally challenging. The potential energy U(X
Æ ) has a relatively xed functional form [1] that is used
by a large number of researchers. The standard form is based on a sum of covalent terms of bonds, angles, and torsions. It also includes noncovalent terms accounting for atomic hard cores, dispersion forces, and electrostatic interactions. A great deal of work was done on the design of the functional form of the potential energy function and on determining a suitable set of parameters. While much more remains to be optimized, current potentials allow for sound simulations of many systems. In this chapter, we take the molecular potential for granted and focus on other challenges that MD simulations face.
